[phenixbb] heavy atom in pdb for refinement
Nathaniel Echols
NEchols at lbl.gov
Fri Sep 11 16:08:59 PDT 2009
On Sep 11, 2009, at 3:54 PM, Pavel Afonine wrote:
>> I have Zn atoms in my pdb for refinement. However, it failed with
>> the following scripts. Do I have to create a libary of this heavy
>> atom?
>
> no, you shouldn't. Zn should be recognized automatically if it is
> properly defined in input PDB file. I just verified that if it is
> formatted like this:
>
> HETATM 2306 ZN ZN D 1 24.598 75.945 -1.390 1.00
> 5.00 ZN
>
> then it works fine. I'm not sure if capitalization is important as
> well as HETATM instead of ATOM - this is something you can try in no
> time.
I'm pretty sure capitalization is indeed important, because I had a
similar problem in both phenix.refine and eLBOW with manganese (MN is
okay, Mn is not).
-------------------
Nathaniel Echols
Lawrence Berkeley Lab
510-486-5136
NEchols at lbl.gov
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